ARS | Publication request: Genetic variability among the brown rust resistant and susceptible genotypes of sugarcane by RAPD technique

Submitted to: Pakistan Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 20, 2011
Publication Date: February 26, 2013
Citation: Muhammad, K., Afghan, S., Pan, Y.-B., Iqbal, J. 2013. Genetic variability among the brown rust resistant and susceptible genotypes of sugarcane by RAPD technique. Pakistan Journal of Botany. 45(1):163-168.

Interpretive Summary: Sugarcane is the second largest cash crop in Pakistan grown on over one million hectares of lands. Infection by red rot, ratoon stunt, and rust disease is the most important reason for yield reduction. We attempted to identify DNA markers associated with the sugarcane rust disease by analyzing the genetic variability among DNA samples from six cultivars. Leaf DNA samples were collected and were analyzed with random amplified polymorphic DNA (RAPD) primers through a chemical process called polymerase chain reaction (PCR). Thirty-three RAPD primers amplified 216 DNA fragments, of which 164 (76%) showed size variability among the six sugarcane cultivars. When the variability was analyzed by numerical computer software, the six cultivars were clustered into three main groups with two subgroups showing significant correlation between genetic variability and disease response. Furthermore, 10 RAPD primers amplified DNA fragments that were distinctive between the rust resistant or susceptible cultivars. The results from this study initiated genetic exploration of different phenotypic classes for possible molecular marker development in sugarcane.

Technical Abstract: Brown leaf rust in sugarcane is caused by Puccinia melanocephala (Syd. & P. Syd.), which is major cause of cultivar withdrawal. We attempted to analyze the RAPD diversity of two discrete phenotypic classes i.e. rust resistant (R) and rust susceptible (S) of six commercially available sugarcane elite genotypes in Pakistan. DNA samples were extracted from these cultivars. The genomic DNA was amplified with 160 decamer primers and 33 of them generated 216 trackable loci with the range of 150-2500 bp. The total polymorphic bands were 164 (76%) and these were used to cluster rust resistant and susceptible cultivars. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) based on Nei’s genetic distance was analyzed by NTSYSpc and showed that six genotypes were clustered into two groups with the range from 63% to 73% genetic distances. This observation indicated the significant correlation between genetic distance and disease. The ten (30%) decamers had shown 100% polymorphism with three polymorphic bands/loci, which were generated in two different discrete groups rust resistant and rust susceptible. In this study we have found 17 cultivars specific loci generated by 11 RAPD primers and cluster analysis revealed three main groups and two subgroups against rust susceptible genotypes to develop characterization of genotypes at molecular level. Additionally, this explored the genetic basis of discrete phenotypic classes in sugarcane genome for marker development.